oppar

This is the released version of oppar; for the devel version, see oppar.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

Outlier profile and pathway analysis in R

Bioconductor version: Release (3.23)

The R implementation of mCOPA package published by Wang et al. (2012). Oppar provides methods for Cancer Outlier profile Analysis. Although initially developed to detect outlier genes in cancer studies, methods presented in oppar can be used for outlier profile analysis in general. In addition, tools are provided for gene set enrichment and pathway analysis.

Author: Chenwei Wang [aut], Alperen Taciroglu [aut], Stefan R Maetschke [aut], Colleen C Nelson [aut], Mark Ragan [aut], Melissa Davis [aut], Soroor Hediyeh zadeh [cre], Momeneh Foroutan [ctr]

Maintainer: Soroor Hediyeh zadeh <hediyehzadeh.s at wehi.edu.au>

Citation (from within R, enter citation("oppar")):

Chenwei Wang, Alperen Taciroglu, Stefan R Maetschke, Colleen C Nelson, Mark Ragan, Melissa Davis. oppar: Outlier profile and pathway analysis in R. doi:10.18129/B9.bioc.oppar, R package version 1.40.0, https://bioconductor.org/packages/oppar.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("oppar")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("oppar")

OPPAR: Outlier Profile and Pathway Analysis in R	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, GeneSetEnrichment, Pathways, Software, SystemsBiology
Version	1.40.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 years)
License	GPL-2
Depends	R (>= 3.3)
Imports	Biobase, methods, GSEABase, GSVA
System Requirements
URL

Suggests	knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	oppar_1.40.0.tar.gz
Windows Binary (x86_64)	oppar_1.40.0.zip
macOS Binary (big-sur-x86_64)	oppar_1.40.0.tgz
macOS Binary (sonoma-arm64)	oppar_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/oppar
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/oppar
Package Short Url	https://bioconductor.org/packages/oppar/
Package Downloads Report	Download Stats